They discuss the microbial community in the feces of healthy horses and those with colitis. In the conclusions, they also discuss the possibility of "fecal transplants" to treat problems in the gut microbiome.

"Bacterial species richness and diversity are thought to be important components of a ‘healthy’ intestinal microbiome. Decreases in richness and diversity have been associated with conditions such as chronic diarrhea and recurrent C. difficile infection (CDI) in humans [24], [40]. Restoration of bacterial diversity and richness is the principle behind fecal microbiota transplantation, an approach that has received much attention recently for successful treatment of recurrent CDI [41], [42]. Surprisingly, equine colitis was not associated with loss of diversity and richness, but further studies using more uniform groups of horses with specific etiologies are required. Microbiota transplantation might potentially be an effective treatment to restore this complex environment towards is considered more ‘normal’." I find it very surprising that they do not discussion "transfaunation" which is basically fecal transplantation in animals. For more on transfaunation see:

And I think they should have / could have mentioned "poo tea" which some old school horse caretakers make for horses with colitis. For more on that I suppose you can watch my Tedmed/Ted talk where I talk about this issue briefly